public override void ExecuteImpl(int threadNum)
{
var pairHandler = _pairHandlers[threadNum];
foreach (ReadPair readPair in _readPairs)
{
var bamAlignmentList = pairHandler.ExtractReads(readPair);
foreach (var bamAlignment in bamAlignmentList)
{
if (_filter == null || !_filter.ReadIsBlacklisted(bamAlignment))
{
_bamWriterHandles[threadNum].WriteAlignment(bamAlignment);
}
}
}
}
private void FlushToBam()
{
OnLog(string.Format("Writing {0} alignments to bam file.", _alignmentBuffer.Count));
var skippedAlignments = 0;
foreach (var bamAlignment in _alignmentBuffer)
{
if (!_filter.ReadIsBlacklisted(bamAlignment))
{
_bamWriter.WriteAlignment(bamAlignment);
}
else
{
skippedAlignments++;
}
}
OnLog(string.Format("Buffer flushed. Skipped {0} alignments.", skippedAlignments));
_alignmentBuffer.Clear();
}